rs10817199

Variant names:

• chr9-111631995-C-A
• rs10817199
• NM_001015882.3:c.336+252C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-111631995-C-A
• chr9-111631995-C-G
• chr9-111631995-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001015882.3(DNAJC25):​c.336+252C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DNAJC25 NM_001015882.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

DNAJC25 (HGNC:34187): (DnaJ heat shock protein family (Hsp40) member C25) Predicted to be involved in protein folding. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC25-GNG10 (HGNC:37501): (DNAJC25-GNG10 readthrough) This gene represents naturally-occurring mRNAs that are co-transcribed products of the neighboring DNAJC25 and GNG10 genes. These transcripts include the first exon of DNAJC25 and the last two exons of GNG10, resulting in a protein that combines the N-terminus of DNAJC25 and the C-terminus of GNG10. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC25	NM_001015882.3	c.336+252C>A		intron_variant	Intron 1 of 3	ENST00000313525.4	NP_001015882.2
DNAJC25-GNG10	NM_004125.4	c.336+252C>A		intron_variant	Intron 1 of 2		NP_004116.2
DNAJC25	NR_037148.2	n.410+252C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC25	ENST00000313525.4	c.336+252C>A		intron_variant	Intron 1 of 3	1	NM_001015882.3	ENSP00000320650.3
DNAJC25-GNG10	ENST00000374294.3	c.336+252C>A		intron_variant	Intron 1 of 2	2		ENSP00000363412.3
DNAJC25	ENST00000447096.1	n.336+252C>A		intron_variant	Intron 1 of 4	1		ENSP00000399325.1
DNAJC25	ENST00000463589.5	n.336+252C>A		intron_variant	Intron 1 of 4	5		ENSP00000464086.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10817199; hg19: chr9-114394275;